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Crystal structure of a deletion mutant (N59) of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QKF PDB ENTRY 2QKF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 297 20 mg/mL protein (in 10 mM BTP pH 7.5) mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 4.6) and 0.6-3.0 M NaCl. Immediately prior to data collection, crystals were harvested and soaked briefly in cryoprotectant solution, comprising 20% glycerol and the reservoir solution, Vapor diffusion, hanging drop, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.36 47.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.058 α = 90 b = 85.744 β = 90 c = 163.187 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 IMAGE PLATE RIGAKU RAXIS IV++ 2009-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 36.66 99.4 0.07 9.8 4.52 91249 91249
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 97.3 0.357 3.4 4.36 8783
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2QKF 1.9 32.76 91174 91174 4579 99.38 0.1906 0.1906 0.1887 0.1868 0.2285 0.2275 RANDOM 28.93
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.49 -0.36 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.939 r_dihedral_angle_4_deg 15.156 r_dihedral_angle_3_deg 15.028 r_dihedral_angle_1_deg 6.437 r_scangle_it 4.971 r_scbond_it 3.083 r_mcangle_it 1.966 r_mcbond_it 1.139 r_angle_refined_deg 0.932 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.939 r_dihedral_angle_4_deg 15.156 r_dihedral_angle_3_deg 15.028 r_dihedral_angle_1_deg 6.437 r_scangle_it 4.971 r_scbond_it 3.083 r_mcangle_it 1.966 r_mcbond_it 1.139 r_angle_refined_deg 0.932 r_chiral_restr 0.08 r_gen_planes_refined 0.01 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7410 Nucleic Acid Atoms Solvent Atoms 717 Heterogen Atoms 18
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction